UniProt

• Alternative protein full names for UniProtKB entries
• Connect patents cited in UniProtKB with those in the patent database at EPO via publication number, whose grant date is more than twenty years in the past.
• Connect patents cited in UniProtKB with those in the patent database at EPO via publication number.
• Construct new triples of the type 'HumanProtein' from all human UniProtKB entries
• Count all isoforms for a given proteome
• Count number of unique Rhea transport reactions annotated in reviewed UniProtKB entries.
• Extracting an UniProtKB primary accession from our IRIs. Is done with a bit of string manipulation. While UniProt primary accession are unique within UniProtKB they may be reused by accident or itentionally by other data sources. If we provided them as strings (not IRI) and if you used them in a query that way, you might accidentaly retrieve completely wrong records.
• Find (Human Genetic) diseases, that are related to a natural variant on the active site of an enzyme.
• Find (Human genetic) diseases that are thought to be related to Enzymes, known to be located in the Mitochondrion
• Find Drosophila enzymes, that depend on more than one transcript (requires cross-references to Ensembl family of resources).
• Find Drosophila proteins, that depend on more than one transcript (requires cross-references to Ensembl family of resources).
• Find GeneID's crosslinked to more than one human or mouse UniProtKB entry
• Find Hydrolases (enzymes that catalyse the hydrolysis of various bonds) that have at least two transmembrane domains
• Find UniParc records whose sequence point to the most database entries
• Find UniProtKB entries with a transmembrane region, with an alanine in the 15 amino acid region preceding the transmembrane
• Find UniProtKB entries with merged loci in Bordetella avium
• Find UniProtKB entries with more than 1 Topological domain annotation
• Find UniProtKB entry which has a protein name 'HLA class I histocompatibility antigen, B-73 alpha chain'
• Find UniProtKB entry, or an UniProtKB entries domain or component which has a name 'HLA class I histocompatibility antigen, B-73 alpha chain'
• Find UniProtKB proteins which are cleaved and contain a domain or component named 'HLA class I histocompatibility antigen, B-73 alpha chain'
• Find all Rhea (only small molecule) that are used in UniProtKB where the annotation has a paper and is tagged having experimental evidence.
• Find all names associated with UniProtKB entry P05067, and if the name is associated with the entry it's domains or its components
• Find all natural variant annotations if associated via an evidence tag to an article with a PubMed identifier
• Find all proteins linked to arachidonate (CHEBI:32395)
• Find all taxonomic records that describe species of the genus Homo.
• Find diseases that are thought to be related to enzymes
• Find enzymes that have at least two transmembrane domains, whose 3D structure is elucidated through X-Ray analysis
• Find enzymes with a Tyrosine (Y) as an active site
• Find enzymes, where the active site is a region affected by mutagenesis and show the comment regarding mutagenesis effect.
• Find how often an article in PubMed was used in an evidence tag in a human protein (ordered by most used to least)
• Find human proteins that catalyze reactions where substrates or product have a Cholestane skeleton
• Find human transporter proteins in reviewed UniProtKB/Swiss-Prot, that are expressed in the liver (Uses Bgee and UBERON).
• Find longest comment text associated with a UniProtKB natural variant annotation
• Find mouse homologs in OMABrowser of human enzymes that catalyze reactions involving sterols (CHEBI:15889). Federating with Rhea and OMABrowser.
• Find taxon records for which one reviewed UniProtKB/Swiss-Prot entry exists. We might expect species, strains, subspecies and isolates in the taxon list.
• Find taxon records that are known to have part of their life cycle in other organisms (e.g. parasite, symbiont, infection)
• Find the Rhea and InterPro combinations in UniProtKB entries.
• Find the co-occurence count of topological domain comment text in UniProtKB entries
• Find the human protein which contains an epitope VSTQ, where T is a phosphorylated threonine
• Find the orthologous proteins for UniProtKB entry P05067 using the OrthoDB database
• Find the release number of the UniProt data that is currently being queried
• Find the similar proteins for UniProtKB entry P05067 sorted by UniRef cluster identity
• Find where disease related proteins are known to be located in the cell
• For the human entry P05067 (Amyloid-beta precursor protein) find the gene start ends in WikiData
• For two accession numbers (ACs) find the GO term labels and group them into GO process,function and component
• Generate a draft human metabolome
• Get the list of UniProtKB entries for the chromosome of proteome UP000000625
• Given an UniProt chain identifier, generate the matching sequence as a FASTA
• How many distinct extinct organisms are represented in UniProtKB
• List Rhea reactions associated with an EC (enzyme classification).
• List Rhea reactions that are not associated with an EC (enzyme classification).
• List UniProtKB proteins with genetic replicon that they are encoded on using the Proteome data.
• List UniProtKB proteins with their associated gene and the gene's ORF label
• List UniProtKB proteins with their associated gene and the gene's names that are used in the field, but not recommended for use by UniProtKB
• List UniProtKB proteins with their associated gene and the gene's preffered name
• List UniProtKB proteins with their associated named gene
• List all InterPro member database signature match start and end for a specific UniProtKB protein.
• List all UniProtKB protein ID (mnemonic) for current UniProtKB entries.
• List all UniProtKB protein ID (mnemonic) that where used in the past for current UniProtKB entries.
• List all UniProtKB proteins and if they are reviewed (Swiss-Prot) or unreviewed (TrEMBL)
• List all UniProtKB proteins annotated to be related to a genetic disease.
• List all human UniProtKB entries and their computationaly mapped potential isoforms.
• List all human UniProtKB entries and their sequences, marking if the sequence listed is the cannonical sequence of the matching entry.
• List the created, last modified, and last sequence update dates for UniProtKB proteins.
• List the proteins encoded by a gene that is located in an organelle other than the nucleus, or on a plasmid rather than a chromosome. In these cases the gene location is stored with encodedIn properties. Note that if a plasmid has several names, they are listed as multiple rdfs:label properties.
• Look for enzymes catalyzing reactions with molecules similar to dopamine, with natural variants related to a disease.
• Look for enzymes catalyzing reactions with molecules similar to dopamine.
• Map a selection of PDB identifiers plus chains to UniProtKB
• Map a selection of UniProtKB accession numbers (ACs) to HGNC identifiers and symbols
• Number of proteins with binding sites for metals or metal sulfur clusters (and experimental evidence for the binding)
• Number of reviewed entries (UniProtKB/Swiss-Prot) that are related to kinase activity
• Predicates and objects, for a given UniParc accession as a subject
• Proteins involved in metabolic diseases in UniProtKB. Using the MeSH concept as a root to find metabolic diseases in UniProt.
• Proteins with binding sites for ligands similar to heme
• Retrieve UniProtKB entries with sequences that are composed of fragments
• Retrieve all protein names, including peptide names, associated with UniProtKB entry P05067.
• Retrieve drugs that target human enzymes involved in sterol metabolism (federated query with Rhea and ChEMBL via IDSM/Elixir czech republic).
• Retrieve drugs that target human enzymes involved in sterol metabolism (federated query with WikiData and Rhea).
• Retrieve entries and catalytic activities in the reviewed (UniProtKB/Swiss-Prot) section that have experimental evidences,
• Retrieve glycosylation sites and glycans on human enzymes (federated with Glyconnect)
• Retrieve human enzymes that metabolize sphingolipids and are annotated in ChEMBL
• Retrieve images of 'Anas' (Ducks) from the European Environmental Agency databases (federated query).
• Retrieve the UniProtKB proteins, their catalyzed Rhea reactions, their encoding genes (Ensembl) and the anatomic entities where the genes are expressed (UBERON anatomic entites from Bgee expression data resource).
• Retrieve the rank and the scientific name of an taxonomic record. Not all taxonomic records have a rank associated with them.
• Select Enzyme Classification (EC) classes that have a protein associated to them
• Select a mapping of UniProtKB enzymes to PDB entries using the UniProtKB cross-references to the PDB database.
• Select a mapping of UniProtKB to PDB entries using the UniProtKB cross-references to the PDB database
• Select all UniProtKB entries that were integrated on the 30th of November 2010
• Select all UniProtKB entries with annotated transmembrane regions and the regions' begin and end coordinates on the canonical sequence
• Select all UniProtKB entries, and their organism and amino acid sequences (including isoforms), for E. coli K12 and all its strains
• Select all bacterial taxa and their scientific name from the UniProt taxonomy
• Select all cross-references to external databases of the category '3D structure databases' of UniProtKB entries that are classified with the keyword 'Acetoin biosynthesis (KW-0005)'
• Select all human UniProtKB entries with a sequence variant that leads to a 'loss of function'
• Select all human UniProtKB entries with a sequence variant that leads to a tyrosine to phenylalanine substitution
• Select all taxa from the UniProt taxonomy
• Select all triples that relate to the EMBL CDS entry AA089367.1:
• Select all triples that relate to the taxon that describes Homo sapiens in the named graph for taxonomy
• Select enzymes that have ligands known to have an allosteric effect
• Select reviewed UniProtKB entries (Swiss-Prot), and their recommended protein name, that have a preferred gene name that contains the text 'DNA'
• Select the Gene Protein Reaction sets for Human (Ensembl Gene, Human UniProtKB, Catalyzed Rhea reactions)
• Select the UniProtKB entry with the mnemonic 'A4_HUMAN'
• Select the average number of cross-references to the PDB database of UniProtKB entries that have at least one cross-reference to the PDB database
• Select the number of UniProtKB entries for each of the EC (Enzyme Commission) top level categories
• Select the preferred gene name and disease annotation of all human UniProtKB entries that are known to be involved in a disease
• Show for a given UniParc accessions which active UniProtKB entries have the same amino acid sequence
• Sometimes it is known that a gene encoding a protein UniProtKB is located on a plasmid or an organelle, but the name of the plasmid is unknown.
• The recommended protein full names for UniProtKB entries
• The recommended protein short names for UniProtKB entries
• Translate a selection of UniProtKB accession numbers into other options using the identifiers.org translating endpoint.
• Translate the global unique identifier for a UniProtKB record into other options using the bioregistry translating endpoint.
• Use ALLIE a service for Abbreviation / Long Form in Japanese and English to search in UniProt using Japanese.
• Was any UniProtKB entry integrated on the 9th of January 2013
• Where are the human genes encoding enzymes metabolizing N-acyl sphingosines expressed in the human body (federated query, with Rhea and Bgee)